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Table 3 Summary of advantages and disadvantages of strategies for direct RNA sequencing of RNA viruses

From: A novel method for the capture-based purification of whole viral native RNA genomes

Strategy type

Employed in

Advantages

Disadvantages

1. Custom adapter

– Keller et al. (2018)

– Highest sequencing specificity

– Rapid turnaround time

– Cannot sequence fragmented RNA

– Foreknowledge of target sequence required

2. Conventional adapter

– Wongsurawat et al. (2019)

– Pre-capture group

– Sequences fragmented RNA

– No foreknowledge of target sequence

– Rapid turnaround time

– Low sequencing specificity

3. Conventional adapter + capture

– Post-capture group

Concentrated post capture group

– Sequences fragmented RNA

– Less foreknowledge of target sequence required

– Higher sequencing specificity

– Increased turnaround time

4. Conventional adapter + host rRNA depletion

– Wongsurawat et al. (2019)

– Sequences fragmented RNA

– No foreknowledge of target sequence

– Fast turnaround time

– Low sequencing specificity